RNAbor statistics

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RNAbor specifications

Information


Unique identifier OMICS_05298
Name RNAbor
Interface Web user interface
Restrictions to use None
Input data RNA sequence, optionally a secondary structure for the input sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Peter Clote <>

Publication for RNAbor

RNAbor in publications

 (6)
PMCID: 5836843
PMID: 29504917
DOI: 10.1186/s12859-018-2018-4

[…] for rna secondary structures, algorithms and tools that calculate the probability distribution of the secondary structures over the hamming distance from the reference structure has been proposed (rnabor [, ], rintd []). if the distribution is concentrated near to the reference structure, the structure is regarded as reliable (i.e. low credibility limit). if there are multiple clusters […]

PMCID: 4808746
PMID: 27110241
DOI: 10.1155/2016/9654921

[…] structure rules as described above, including a minimum length of hairpins of 3. the number of possible neighbours is bounded by o(n 2), where n is the length of the structure. the implementation rnabor for studying statistics of rna structural neighbours has been introduced in []. rnabor computes the number and boltzmann probabilities of all structures having base pair distance d to an input […]

PMCID: 4521916
PMID: 26230932
DOI: 10.1371/journal.pone.0134262

[…] such as in phmm [] and the advanced infernal, which also incorporates covariance models [–]. other approaches include boltzmann probability of rna structural neighbors for riboswitch detection as in rnabor []. genome-wide measurement of rna secondary structure by high-throughput sequencing [] can also be useful in attempting riboswitch discovery. on the topic of searching for new riboswitches […]

PMCID: 4304215
PMID: 25560710
DOI: 10.1186/1471-2164-15-S10-S6

[…] practical problems. the first example is the distribution of the hamming distances from a reference structure. a practically equivalent algorithm and its acceleration have been implemented as rnabor by [] and [], while we have reconstructed the algorithm by deducing from our general principle. the second example is the exact distributions of 5ʹ - 3ʹ distance. conventional methods […]

PMCID: 3526635
PMID: 23284639
DOI: 10.1371/journal.pone.0050506

[…] to predict the location of riboswitch expression platform candidates. a web server is available at http://bioinformatics.bc.edu/clotelab/fftbor/., in , we developed a dynamic programming algorithm, rnabor, pronounced rna neighbor, which simultaneously computes for each integer , the boltzmann probability of the subensemble of structures whose base pair distance to a given initial, […]


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RNAbor institution(s)
Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden; School of Computing Sciences, University of East Anglia, Norwich, UK; Department of Biology, Boston College, Chestnut Hill, MA, USA

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